Instinct
by Keegan Paige
Summary: After accompanying Sheppard’s team to a peaceful planet for negotiations, Elizabeth gets much more than she bargained for. Will John be able to save her? What legnths will he go to? Add action and adventure in later chapters.Shweir. Chap 11 up!
1. The Beginning

_Title:Instinct _

_Summary: After accompanying Sheppard's team to a peaceful planet for negotiations, Elizabeth gets much more than she bargained for. Shweir, of course, though very angsty…_

_Category: Angst/romance, of course! _

_Disclaimer: I don't own Stargate Atlantis or any of the characters (except the ones I made up)._

_A/N: Wow! I didn't think I could actually do this, but here it is. My first Atlantis fic. This is also the first fic I've ever wrote that incorporates a character I made up. Pardon the cliché, but it looks like I've taken out two birds with one stone. Wait, this is also the first time I've had flashbacks in a fic. Well, this is just new all over, isn't it! Now, unlike the majority of my other fics, this is definitely not a one-shot. Oh, btw, if anyone wanted to know, I am currently trying to continue my SG-1 fic "Release", but it has proved to be a lot more challenging than I originally thought. So pass the word around!_

_A/N2: Sorry for the crappy summary and title, I really suck at thinking those up. _

_Instinct_

_Chapter 1: The Beginning _

It was late when Lt. Colonel John Sheppard walked up the stairs to Dr. Elizabeth Weir's office. Although it was around two in the morning, he didn't need to wonder whether or not she was in her office. She _always_ was; especially when something was bothering her. The latter pertained to the recently passed situation. Just as he thought, he found her sitting at her desk, head titled and resting on top of her raised hand while starring at the computer screen. He smiled when he knocked on the glass before entering.

"Hey, what're you doing up still?" He asked, acting as if he didn't know. Though Elizabeth saw right through the act, she played along.

"Not tired." She answered casually.

"Really? After everything that's happened lately, I thought you'd be exhausted."

"You thought wrong." She said carefully.

_3 days ago _

The sun emerged through the clouds shining down on a dirt road. Two people walked slowly down the path surrounded only by flowers and sunshine.

"It's wonderful out here." Elizabeth said to her companion, smiling.

"Yes, but it's even more wonderful at night. It's so beautiful when the first stars appear, sometimes you can forget about where you are." He said grinning while turning to face her.

"I know what you mean. Sometimes when things are hectic in Atlantis I stand out on one of the balconies overlooking the ocean. Everything is so calm and peaceful out there that I can just get lost." Elizabeth laughed, "Dimitri, I can't believe I told you that."

Blonde haired and blue eyed, Dimitri Logan was a native of the planet they were currently visiting. He was also "the ruler" of the small colony, so Elizabeth immediately connected with him.

Continuing she added, "The only other person who knows is…" She was interrupted when a shout was heard in the distance. As the calling came closer she recognized the voice and figure as it emerged from the tree line a short distance away.

"Elizabeth!" The man called again as he spotted her, before quickly jogging over to where she and Dimitri were standing. "Jeez, there you are. I've been looking all over for you." He stated, a bit annoyed as he looked over Dimitri. Elizabeth turned to Atlantis' Military leader looking quizzically, "Is there a problem John?"

"Ah, no, not really. I just wanted to discuss something with you." He caught and kept Elizabeth's glance before continuing, "But, _apparently_ it can wait." John ended smugly, with a noticeable nod toward Dimitri.

"Actually, I think I'd better start heading back now." Dimitri retorted, though smiled sweetly at Elizabeth.

"Elizabeth," Dimitri bade farewell as he turned and walked slowly up towards the village, angrily. Elizabeth couldn't help but frown a bit. She had clearly seen the uneasiness between John and Dimitri from the moment they met. And it hadn't worried her, until now.

"Hey. Hey," John said placing a firm hand on her shoulder to shake her a bit. "You ok?" He added when he finally got her attention.

"Hmm? Oh, sorry. Yeah, I'm fine." Elizabeth answered giving a fake smile. Unfortunately, John noticed and continued to question her.

"What's bothering you?" He asked bluntly, his hand unmoved from its position. Elizabeth knew she couldn't get out of this one; though part of her didn't want to. She made a quick glance over the surrounding area before looking up at John. "Care to take a walk?" She was so dazed; she hadn't even noticed his hand on her shoulder.

A short while later they found themselves on the established balcony. "Their" balcony, as it had unofficially been named by many Atlantis personnel (a/n: aka, the Shweir fans!). The wind blew slightly and refreshingly. Elizabeth placed both hands on the silver railing and gripped the metal tightly while slowing breathing. After a second she turned to face John, keeping one hand on the rail. She flashed a small smile before opening the conversation. "You remember Dimitri, right?" Of course he remembered him, Elizabeth knew, but it seemed there was no other easy way for her to start.

John could have been sarcastic in his reply, but all he said was, "Yeah."

"You also remember that he contacted me earlier?" It was more of a statement than a question, but John replied anyway.

"Yeah, you didn't tell me what he said." By now he had an idea of what this was about, and he didn't like it.

"He wants me to come back." Elizabeth said plainly, looking up at the purple and pink sky to avoid his gaze. John shifted his weight turning from her to face the horizon. It was his turn to grip the railing. He, in no way, wanted to return to that planet, though he asked, "When do we _have to_ leave?"

"I meant alone." She said simply, making a sideways glance towards him.

"Well, you do seem to make an impression on people." He attempted to joke. Elizabeth didn't find it humorous.

"John," She said firmly. "I know that you don't like him, but we can't have an alliance with his these people…"

"Elizabeth," He said cutting her off. "This isn't about making an alliance, it's about you. You just said it, obviously this _visit_is just for him." John stared straight at her.

"And I won't let you go."

_A/N:As always, I love reviews! Please help me out by pressing that little button and giving me your thoughts. Thanks! _


	2. Trust

_Instinct_

_Chapter 2: Trust_

"Excuse me?" Elizabeth said authoritatively, glaring sharply at Sheppard. This conversation, well argument now, had obviously taken a turn for the worse. She knew he wouldn't like what Dimitri had to say, but she hadn't expected this reaction. "Since when does John Sheppard decide…"

Again, he cut her off, "I don't, but there's just something about him." He started, raising his hand toward her. Taking a breath he finished, calmly "Elizabeth, I just don't trust him." Elizabeth was a bit confused; was he trying to protect her or was he, dare she think it, jealous?

Curious, she cautiously asked, "John, why is this bothering you so much?" She looked at him, an almost pleading look on her face.

John paused a moment before returning his eyes to her. He slowly began, "Because I-"

"Dr. Weir, you're needed in the control room." They were interrupted when a voice came over Elizabeth's radio.

"I'm on my way." Elizabeth said slightly agitated. Exchanging almost sympathetic glances, they left the balcony and entered Atlantis side by side.

"What's there problem, gentlemen?" Dr. Weir called as she entered the control room. The approaching airman explained, "A message from Dimitri Logan arrived a minute ago, ma'am." He began pressing various buttons, and then the message came up on the screen. The scene shocked everyone in the control room.

"Elizabeth," Dimitri tried to begin. He was frantic, looking over his shoulder every couple seconds. His breathing was heavy, sweat trickled down the side of his face. "Elizabeth, I don't have much time. We are under attack. Please help us!" Glancing one more time over his shoulder, he froze. "NO!" The last thing Elizabeth saw was Dimitri fall to the floor after hearing a shot in the background; the message ended there.

Sheppard was speechless while he stared at the screen; part of him just didn't quite believe this. Who in the galaxy would attack a tranquil and well protected planet? It couldn't be the Wraith, they would've known if they were in the area. So, what was going on?

"Colonel, I need you to assemble your team." Elizabeth directed towards Sheppard. John wasn't happy and it showed.

"Dr," He strained, if she was going to go formal, then so was he. "I don't believe we should just rush in there. We don't know who we'd be up against. I can't risk my team."

Elizabeth understood every bit that he was saying, but she couldn't get past what she just saw in the video. Dimitri could be lying on the floor bleeding to death, if he wasn't dead already. Her emotions were making her act hastily and that was a problem. Calming herself, Elizabeth looked up at John. "IfI sent two teams with you, would that be enough?"

"I think we'd be able to handle it, yeah." John said against his gut feeling, he would do almost anything for her.

"Then you have a go. Dismissed." Elizabeth concluded. John left the control room to grab his gear and team, never looking back.

_A/N: Sorry for the short chapter, the next one should be longer. Again, replies are great! Thanks so much for those who did reply!_


	3. Confusion

_Instinct_

_Chapter 3: Confusion_

From the minute he stepped through the gate, Sheppard's bad feeling continued to grow until it was almost unbearable. This had to be a trap; there was no way that this planet they had left merely three days ago was under attack. Despite everything that had happened with Dimitri, the people on this planet were very peaceful and careful about protecting their planet.

_flashback_

"Are you telling us that the Wraith have never been here?" Elizabeth Weir excitedly questioned, sending a surprised look toward Sheppard. John sent a grin back, obviously feeling the same thing as Elizabeth.

"Yes. To our knowledge they do not know that we exist. Thanks to the force-shield Dimitri made." Nora answered. Nora was a friendly and simple woman from the village that had offered to exchange information with the new visitors.

"This is extraordinary!" Elizabeth said happily.

"Excuse me, I must finish my work now." Nora said disappointedly. Elizabeth thanked Nora for her help, then turned to John when she walked away.

John, do you know what this could mean?" Elizabeth knew the answer already, but asked anyway.

"That we could have an alliance with these fine people and a free planet. Plus, if the Wraith haven't found out about this place, there's a chance that the closest surrounding planets have been untouched too." John recited what he had thought up a minute ago.

"Nicely said, Col." Elizabeth said smirking.

John replied with a devilish grin, making Elizabeth blush slightly. They continued to glance at each other childishly as they made their way to the gate, following the setting sun's path.

Shaking the scene out of his mind, John continued his journey onto the village along with his crew and two other teams covering their sixes. They arrived a short time later to find the absolute opposite of what they were expecting. The planet was completely derelict; no one was there. Exploring some of the houses John felt tried to figure out what had went down. After a while the group gathered in the 'town square' to check in.

"It looks like they just packed up and left, sir." Major Lorne informed Sheppard

"Yeah, that's what I thought too. Any ideas?"

"Who ever attacked them might have made them evacuate; getting rid of all the evidence." Lorne guessed.

"Possible. Or it could've been a set-up from the beginning." Sheppard said casually.

"You still don't trust them. Anyone in particular, sir?"

"That guy."

"That guy? Dimitri Logan, you mean. Understandable, I guess."

"What's that supposed to mean?" Sheppard shot back offensively.

"Oh, nothing, sir. Just forget about it." That was exactly the wrong thing to say to John Sheppard at this moment.

"Major, are you withholding information from a senior officer?" Yes, Sheppard had a way with words.

"Just a rumor I heard, sir."

"Concerning?"

"Your, well, you and Dr. Weir's relationship. It's just that a lot people seemed to notice that you've been very protective of her recently."

"Well, I wouldn't want the good Dr. to get hurt, especially while off world, would I?"

"Of course not. Can I ask you a personal question?" No, John thought automatically. Unfortunately curiosity overruled instinct and John complied, "sure."

"I heard Logan's been putting the moves on Dr. Weir. What are you going to do about that?"

"Apparently, I won't have to do anything; someone's already done that job for me. He's disappeared."

"Wow. Uh, one thing though, we could check the DHD and maybe track them down."

"Don't bother. Anything else you care to share before we head back?"

"No, sir."

With that settled they headed back to the gate, concentrating on the real problem at hand.

_a/n: Yeah, very uneventful chapter, sorry. But there was an important conversation between Lorne and Sheppard! The next chapter is better, I'm sure of it. Please give me a review, you know you want to!_


	4. Effects

_Instinct_

_Chapter 4: Effects_

As always, Elizabeth Weir called a debriefing meeting after John and the teams returned from the planet. She was confused, they hadn't brought anyone back and none of them looked the least bit upset. In fact, they looked comfortable. What had happened to everyone? Were they dead? Who was responsible? Where was Dimitri? Questions swirled ferociously causing an extreme headache to overtake her for a few minutes before the teams entered the room. She anxiously awaited their arrival.

"What did you find colonel?" Elizabeth started the debriefing with a question intended for Sheppard.

"Nothing, actually."

"What do you mean?"

"There was actually nothing there, ma'am. The village was still intact, but the people had vanished." Lorne filled in.

"How can that be possible? We all saw the tape."

"There was no evidence of an attack. So, the validity of the tape is another question we have no answer to." Sheppard replied.

"Really? You think it isn't real?" Elizabeth asked.

"It's possible." Sheppard shrugged.

"Hmmm…can we track them using the DHD?" Lorne shifted uncomfortably in his chair, and Elizabeth noticed.

"Do you know something major?"

"Um." He shot a glance toward Sheppard, as if asking him if he should continue. Sheppard simply nodded his head to the side. "Ma'am, Colonel Sheppard told me not to bother."

"Did he?" She asked accusingly, turning her chair to face John's direction.

"Yes, ma'am."

"Did he give you a reason why?"

"It was implied."

"What was?"

"That he didn't have to worry about protecting you now that Logan was gone." Stunned she kept quiet for a moment, then turned back to Lorne and the other personnel in the room.

"Thank you major, you're all dismissed." John stayed seated; he knew he wasn't going anywhere.

One the room had been cleared Elizabeth turned back to Sheppard with disbelief in her eyes. John spoke casually, "You don't look too happy."

"Oh, that's good. I'll have to get you an award for best understatement of the year." She threw back sarcastically.

"Thanks, I'm honored."

"God, John. What the Hell has gotten into you!" Elizabeth said appalled.

"Awareness."

"Of what?"

"That everything you've done lately has been driven strictly by emotions. You saw that tape and you were ready to send me on a suicide mission. You're way too close to him. Or should I say were?"

"I thought we already discussed this, colonel. You are not the one who decides…."

"When it affects the lives of people I care about I do."

"You're very close to crossing a line that you can't come back from, Colonel!"

"What, like you did three days ago?" Elizabeth knew exactly what he was talking about.

"Oh, please, I wasn't even close…" She raised her voice, angry.

"If I wasn't there you would have ended up in his…" Sheppard shouted back.

"Enough! Colonel, I suggest you leave. Now!" Elizabeth commanded. John took the advice. He stood up, shoved the chair in and stormed out.

_a/n: Ooooh, what did Elizabeth do! Anyone think they know? Reviews please!_


	5. Compliments

_Instinct_

_Chapter 5: Compliments_

_a/n: This chapter is one big flashback. It's important you know that! _

John, Elizabeth, and Dimitri were seated around a small round table in a comfortable village house. Elizabeth conveniently sat between Sheppard and Logan. Not what John had wanted, of course, though on the other hand he was just waiting for Dimitri to make a wrong move.

An intricately designed gold chalice had been placed in front of the unusual trio. It contained a tasteful red liquid resembling one of the fanciest wines from Earth. They had already gone through one glass. A toast was made.

"I'd like to propose a toast to the both of you. For now you may be guests, but hopefully in the near future you can be considered close friends. If not for your courage, we'd have never met. And for that I'd like to extend a special thanks to you, Dr. Weir."

'Cheers' went all around.

"Mr. Logan, that was extremely kind of you, thought I don't believe I need any more recognition than anyone else."

"Oh, don't put yourself down. You're a very special woman Dr. Weir and please, call me Dimitri."

"Why thank you, Dimitri. Elizabeth would be fine."

"You're very welcome, Elizabeth."

By this point John was rolling his eyes every time Dimitri opened his mouth. He couldn't believe that Elizabeth was going for this. Flattery had never worked on her, unless it came from himself. He could always make her smile, causing her to look down bashfully, as he broke through another one of her carefully constructed walls. John had a way with her; she was different than any woman he had ever been with. Ok, so technically he wasn't _with _her, he reminded himself, but they were pretty damn close …friends he meant. This talk from the other man was bothering him; finally fed up enough he interrupted.

"Do you use 'very' in every sentence?" Dimitri had been wondering when Sheppard would chip in.

Does it bother you, colonel?" Dimitri quipped nonchalantly.

"Only when you forget the most important characteristics." Sheppard said irritated. Elizabeth raised her eyebrows towards John quizzically as if to ask 'what are up to?'

"Care to fill me in on something I've missed?" Dimitri joked.

"Don't mind if I do. Quite a few things actually; Elizabeth is a 'very' smart, talented, and graceful woman. Not to mention 'very' beautiful. In my expert opinion, she's damn perfect." John gave Elizabeth his bedroom eyes and handsome smile causing her to blush. For a second she was at a loss for words, yet content in finding herself smiling back at John. Facing reality she reluctantly pulled her eyes away. Elizabeth was about to speak when he spoke again.

"It's getting late; we better get moving before it turns dark."

"Of course." Dimitri sneered. Angry Sheppard had showed him up.

Standing up, John followed close behind Elizabeth all the way to the gate. Yet again she found herself at a loss for words.

_a/n: I would have put it with chapter 4 but I didn't want a really long chapter in the middle of short ones. Thanks! Review please!_


	6. Downfall

_Instinct_

_Chapter 6: Downfall_

Elizabeth remained a few moments longer after the debriefing, trying to sort out everything that had just happened. She let herself sigh while covering her face with her hands. Clearing her mind she stood up and walked out, only to be stopped by a familiar shadow leaning against the doorframe. Inevitably, it was none other than John Sheppard.

"Um, hey?" John inquired nervously, receiving an unfriendly look from the woman in question. He certainly couldn't blame her for what she was feeling. He had almost crossed the line. _That_ line.

"Is there something you needed, colonel?" She chided, folding her arms across her chest. Elizabeth didn't want to talk to him, but out of courtesy she listened. Even if he didn't deserve it.

"Look, I'm really sorry about what I said in there. I didn't mean to hurt you or upset you. It makes me angry to think that…" John paused; this was not the right time to finish that sentence, so he avoided it. He wasn't ready to admit what he felt, especially if he didn't know what it meant exactly.

"…anyway, I was just wondering if we could forget everything." He rambled.

"It's not that simple." A cold remark thoroughly deserved.

"It could be." John countered with hope. His sense of humor was incredible, she thought.

When he started talking again he looked down, missing Elizabeth's unexpected wince. Her face tightened in pain.

"I know this sounds weird coming from me, but…"

"John." She whispered shakily, though it wasn't loud enough.

"…I just want you and me to be able to-"

"John!" She interjected as forcefully as she could, finally catching his attention. Feeling queasy she gripped the side rail, though weakly.

"What's wrong?" John asked sincerely worried, rushing to place a careful hand on the side of her waist.

The question went unanswered as Elizabeth slipped out of consciousness and into John's protective arms.

Two hours later John still found himself pacing back and forth on the outskirts of the infirmary room. Plagued by one repeating image while he kept a close eye on the closed white curtain, where he knew she was. He tried to think of any possible solution, but John Sheppard was no doctor and he knew it. This time it was all up to Carson as the image played in his mind again.

* * *

The instant Elizabeth Weir had crumbled into his arms one of his greatest fears, since arriving at Atlantis, had come to life. How ironic. The stunning and fearless leader lay defenseless, in his arms nonetheless. Shock was only one emotion on a list of many that he had felt and still continued to feel. To Sheppard time seemed to slow as he reached out grasping Elizabeth and cradling her against his chest while kneeling on the floor. He felt her go completely limp; motionless after her arms fell to the sides. Her face had already begun to lose its vibrant color. "Elizabeth," he gently whispered trying to wake her from the spell. When a curl of brown hair tumbled down onto her face he pushed it back delicately. How could this happen? What was wrong with her? All questions went unanswered. The only thing that gave him hope was the sound of her breathing in his ear as her head rested carelessly on his strong shoulder. He hated seeing her like this. Out of nowhere time returned to its normal pace as John yelled into his radio to Carson Beckett. Swiftly he'd ran to the infirmary; Elizabeth oblivious in his hold.

* * *

Carson's voice pulled John out of the nightmare. John looked around and noticed the curtain was still closed. He immediately tensed at the sight.

"Are you alright, lad?" The Scot cautiously voiced. Carson knew he wouldn't get an answer so he didn't push it. It was a stupid question anyway; he could clearly see that Sheppard wasn't well.

"How's Elizabeth?" John asked sensing something wrong. Carson could only give Sheppard a blank face, causing the feeling to worsen. "Carson, what is it?" He asked strictly.

"I'm sorry, Colonel. We don't know what-"

"Did she…?" John interrupted, fear in his voice. The question didn't need to be asked in its entirety, the meaning was implied.

"Oh, no! She's alive." Carson couldn't believe that Sheppard had actually feared the worst.

"Is there _any_ particular reason why you didn't think to say _that_ first!"

"I thought you…you were that worried?"

"Scared to death. Carson, she _collapsed_ in my arms." Beckett knew John wasn't that comfortable expressing his feelings so he moved on to more important matters.

"Then you would know if she was doing anything unusual?"

"We were arguing, but we've done that before."

"I don't believe this is stress related. In any case, it wasn't your fault, lad. There was nothing you could do." Carson explained politely patting John's shoulder. Beckett was about to walk away when he saw Sheppard still standing in the same spot.

"You can see her now."

_a/n: Oh, no! What's wrong with Elizabeth? Thanks goes to everyone who has reviewed or read the story. Extra thanks to my beta, SGAngeL._


	7. Revelations

_Instinct_

_Chapter 7: Revelations_

John quietly entered the white curtain only to find himself hurting more. Elizabeth Weir lay motionless on an infirmary bed, though in spite of her condition, her authoritative presence remained. John walked closer to her bed, every step becoming harder than the last. He didn't want to see her like this; this wasn't Elizabeth. When he reached out to touch her hand he was shocked at how cold she was. He kept a hold of her hand hoping in some way that his warmth would wake her, though deep down he knew it wouldn't. John sat down on the edge of the bed carefully and began to speak to the woman lying next to him.

"Hey, Elizabeth. You know we're gonna figure this out, right. You'll get through this." John paused for a second letting out a short laugh, "Wow. And I thought you needed help with your bedside manor." There was no response. He took time to look around the small space that held her in. It was so wrong for her to be here. If anyone should be here it was him.

"Atlantis is waiting; this city needs you, the people too." It was the truth and John Sheppard fully believed it. She deserved so much more than she ever received. Well, that was an understatement. Going quiet he found himself simply staring at her pale face; lost in silence. The visit was interrupted when a small 'ahem' was heard behind him.

Sheppard turned cautiously; he hadn't heard anyone approach. Was he that focused on Elizabeth that it blocked his senses? The man standing behind him surprised John. He hadn't expected him to show up this quick. Then again, he didn't know how long he'd spent with her; all time was lost the moment she called his name. He slowly looked back to Elizabeth and reluctantly let go of her warmed hand. There was so much more he wanted to say to her, but the company he now had barred that from happening. Standing to follow the man, he paused to look her over one last time.

_Meanwhile in the control room…._

Rodney McKay ran to the computer as he saw the chevron's lighting up around the Stargate. "Raise the shield!" He commanded the airman next to him. When the man turned to him with a shocked expression he knew they had a problem.

"It won't rise." The airman said trying anything he could think of.

"Wonderful. Move out of my way." Rodney said practically pushing the airman to the floor. Chevron 6 locked….7….

"Why won't this work!" Rodney shouted to no one in particular as he scrambled to fix the shield. His efforts were lost when the 'kawoosh' of the Stargate's wormhole surged forward. What was even more shocking was the figure standing in the center of Atlantis.

* * *

"Is she alright?"

"She will be."

"I saw the way you were…sorry, I interrupted you didn't I?" The man eyed Sheppard hinting towards the infirmary room they were standing outside of.

"I was just… uh, what are you doing here…sir?" John cleverly avoided the question.

"As of now, I'm taking control of Atlantis." Colonel Steven Caldwell answered firmly.


	8. Changing Times

_Instinct_

_Chapter 8: Changing Times_

"What?"

"Atlantis is under my command until Dr. Weir recovers."

"Thanks, but I think I can handle it. I'm the leading military personnel here so it's my job."

"Only if I'm unavailable to stay on Atlantis. You forget Colonel, I do outrank you."

"I understand that, _sir_, but in this situation we may need the Daedalus' assistance."

"And that can be taken care of when necessary. Right now Atlantis requires a stationary leader. You will have to continue on your missions while I stay here and keep everything in order. This situation has to be cleared up." John clearly looked agitated. There was nothing he could do.

"She's in good hands, Sheppard. You don't have to worry about her." Caldwell continued, noticing Sheppard's glances towards the infirmary.

"Elizabeth is a top priority. She needs…."

"She'll be taken care of. You said it yourself, she'll be alright." Caldwell said sternly. He didn't know why Sheppard was so paranoid about Dr. Weir's condition. It was true, they didn't know what was wrong, but how many times had they faced a blind situation and made it out alive? What John said next surprised him the most.

"Ok. But if there's so much as a scratch on her-" Caldwell would have interrupted, but Rodney's voice on the radio stopped him.

"Sheppard, we have a problem in the control room!"

"Can it wait?"

"Oh, no you'll want to see this."

"What's so important, McKay?"  
"He's here. Dimitri Logan is here."

"I'll be right there." Sheppard called, running beside Caldwell to the control room.

Dimitri kneeled on the floor trying to catch his breath. Everyone stood still until Rodney voiced, "Don't you all have something to do?" Reluctantly they shuffled away as Carson ran through the crowd. Rodney followed him down the steps that led to the believed to be dead man. No one had the slightest idea what was going on; they had all seen the tape, seen him fall to the ground. There was no way he could have survived, let alone escaped. Yet there he was, kneeling in the heart of their very city.

"Where's the wound, lad?" Carson asked helping Dimitri on to a stretcher. He was horrified when Dimitri removed blood stained hands from his abdomen. Three entry wounds could clearly be seen from the holes in his crimson red shirt.

"Oh, dear." Was all Carson could manage as he rushed him to the infirmary.

Sheppard and Caldwell arrived just in time to see Logan being pulled onto the stretcher and whisked away. Rodney spotted them and ran up the stairs to meet a visibly angered Sheppard.

"What the hell is he doing here?"

"I don't know, the gate activated by itself."

"Why didn't you raise the shield?"

"I _tried_, but we were too late. He must have blocked it from the other side somehow." Rodney emphasized on the word tried.

"Wasn't Mr. Logan presumed dead?" Caldwell stepped in, breaking Sheppard and McKay up.

"That's what we had thought after the video feed came in."

"I never trusted that tape. Something's wrong." Sheppard said.

"Besides a man bleeding to death in the infirmary that we had already thought was bleeding to death or dead…yes, something's odd about all of this." McKay chimed in, only to receive a glare from Sheppard.

"Well, I suggest we get to the bottom of it. Inform me the minute Mr. Logan wakes up." Caldwell ordered before walking off.

"Uh, what's he doing here?"

"He's in charge."

"Oh, huh." Rodney whimpered, scuttling back to his work.

John was the first one there when Dimitri regained consciousness. Dimitri seemed uneasy at Sheppard's calmness. He knew hatred still ran inside him, so why was he so laid back?

"Colonel Sheppard?" Dimitri questioned groggily.

"Mr. Logan."

"I just wanted to…thank you...for helping me."

"We didn't exactly have a choice. You showed up at our doorstep without warning."

"Yes. I'm sorry to just show up. I had assumed that you received my message." Sheppard refrained from retorting with 'you know what they say about assuming'.

"We did" he answered instead.

"Then you sent help for my people?"

"Yeah, little problem there, the village was empty when we got there."

"But they we all there when we were taken."

"Taken?"

"Yes. A group of men grabbed me and some others. They ordered us to go through the Stargate with them. We had never seen them before and with their unexpected arrival we had no time to defend ourselves. They made me record the message later."

"That tape wasn't made that long ago, how did you escape so quickly?" It was obvious Sheppard didn't believe his story, though Dimitri had an answer for his questions.

"Five of us were taken. The others distracted them while I ran to the Stargate. They said it would be best if I made it back. Unfortunately, I was the only one to make it."

"Well, my condolences."

"Thank you."

"You're pretty good. There's only one problem with your story." Sheppard said ready to exit, "You never knew Atlantis' address."


	9. Emotions

_Instinct  
__Chapter 9: Emotions_

_A/N: Hey, sorry it took so long. My computer has been giving me problems, grrr…  
__Also, thanks to everyone who has reviewed, it means so much to me! Oh, and big thanks to my beta, SGAngeL, you rock. _

John Sheppard found himself in a familiar place as he stood in front of Elizabeth's office. But this time was different, he knew the minute he saw Colonel Caldwell sitting in her chair. Everything about the image in front of him was wrong. The only person who ever belonged there was Elizabeth Weir. He didn't knock to alert the man to his presence; he just stood in the doorframe, a sorrowful look on his face. For once he was hesitant before entering the office. He couldn't help but imagine seeing Elizabeth sitting there, turning her face upwards and smiling shyly. The vision faded when Caldwell spoke.

"Do you need something, Colonel?" Sheppard cleared his head then entered. Usually he would stand next to the desk or even sit on the edge, but today he stood uncomfortably in the middle of the room.

"I wanted to apologize for my earlier behavior, sir. It won't happen again."

"See that it doesn't."

John nodded as he turned to leave but was stopped when Caldwell caught his attention.

"Relax, Sheppard, I'm not going to redecorate her office or anything." The colonel said, looking up from the computer screen for the first time.

"I know." He said casually.

"You really do hate seeing me here, don't you?"

"No, just dislike immensely." Caldwell let out a small laugh. John Sheppard did have a sense of humor.

"If it means anything to you, I don't like taking Dr. Weir's place. She runs this place exceptionally well, better than I ever could have." John smiled; he didn't have a response. He stood for a second, wondering if Caldwell really meant what he said..

"Was there something else you needed, Sheppard?" After a moment of heartfelt words, it was back to business. Colonel Caldwell couldn't have himself run by emotions.

"No, but, uh, thanks." John left hardly believing he had just thanked him.

Elizabeth had been moved to a private room out of courtesy. John had pushed for it, everyone understood why. By now it was habit now to visit Elizabeth any chance he got. Whenever John wasn't in dire need of defending Atlantis he was at her bedside. He often held her hand, regardless of who might be near; even a certain Colonel's looks didn't bother him anymore. So it wasn't at all strange to find that John was currently stationed next to his top priority in the middle of the night, his hand wrapped around a small, frailer one. As he did every night, he took a few minutes just to look her over, making sure she was exactly the same as when he had left her mere hours ago. Of course nothing was going to be wrong, he assured himself. And nothing was, as always. With his free hand he reached up and gently pushed a loose curl away from her face, making him smile.

"You really oughta' do something about that, it drives me crazy." John joked about almost every thing with her, it eased the tension. He found that more and more of the one-sided conversations had jokes replacing the ever popular, 'you're going to make it,' speech.

"Colonel Sheppard?" A small voice was heard from atop the table, where his radio was resting. Every time he sat with her he took his jacket and radio off. He hated being interrupted, but he knew he couldn't do anything to change that. John had to remind himself that other things were going on in the galaxy and that they never stopped to rest.

"I'm here." He answered the call softly.

"Sir, Mr. Logan would like to speak to you."

"Give me a minute."

"Of course. I'll tell him you're on your way." John sighed placing her hand carefully back at her side. "I have to go, Elizabeth. I'll be back later." Standing, he hesitated for a moment before leaning over and placing a tender kiss on her forehead. He hadn't planned on doing that, it had just happened. He hovered above her for a second, whispering, "Elizabeth, how do you do that to me?" Forcing himself up, he grabbed his radio and jacket before looking back to her once more.

Reaching the well-known infirmary, John stood at the foot of Dimitri's bed with a straight face.

"Colonel Sheppard, I've been waiting for you."

"I was busy."

"I've been meaning to ask you, where is Elizabeth?"

"_Dr. Weir_ is…occupied at the moment. There's a lot of stuff going on, we can't afford to take her away from her work."

"I understand, after all she is the leader here."

"Yes, she is." A small silence followed before John spoke again.

"So, figured out your story yet?" Sheppard asked sarcastically.

"It isn't a story. Many of my people saw you leave, they remembered what symbols you pressed on the device."

"Hmmm...I've got to ask you, why are you trying to be so sincere? When I was on your planet you clearly showed a different side to me."

"I know I was harsh; I didn't really think that we needed anyone's help. But Sheppard, I've realized my mistakes and I ask for your forgiveness."

"I'll have to think about that." He said giving a charitable smile, "Back to the point, what are you doing here?"

"I need your assistance."

"For what?"

"I wish to return to my planet, to search for my people."

"Well that would be a wasted trip. I already told you no one was there."

"You aren't aware of our…secret places, Colonel. If my people are still alive they'd be there and they won't come out until I return."

"If you're just going to retrieve your people why do I need to be there?"

"A simple precautionary measure; I wouldn't want us to be attacked again."

"Of course not."

"I understand your hesitation and distrust, but I assure you that those… tense exchanges between us was just envy getting the better of me."

"Are you trying to say that you're jealous of me?"

"You have quite a lot to be envious of."

"Care to share?"

"Well, Elizabeth for starters." John visibly tensed when he heard Dimitri use her name again. Why was he doing this?

"And what would give you that idea?"

Dimitri smiled, he knew John was playing with him, "The way you were around each other; your protectiveness of her when I was near. The looks, the comments; don't try to deny it Colonel, everyone noticed."

"Look, not that any of this is your business, but Dr. Weir and I are friends. Closer than some, but that's it. And for your information, I'm protective of everyone I care about, no matter what degree."

"I see, no offence was meant. I must have misinterpreted your actions." Dimitri decided to play along.

"Apparently." He hated lying about how he felt about Elizabeth, but there was no way he was going talk about it with this man.

Dimitri moved on, pleading, "Colonel Sheppard, please accept my offer. My people are counting on you."

"I'll see what I can do."

Colonel Caldwell met Sheppard as he was leaving the infirmary.

"What did Mr. Logan have to say?"

"He asked if I would accompany him to his planet when he's out of the infirmary. According to him, his people are there, though in hiding."

"Then I suggest you get ready. I was just informed by Dr. Beckett that he's getting ready to release him."

"Honestly, I'm not sure I should."

"You still don't trust him?"

"No."

"This wouldn't have anything to do with Dr. Weir, would it?" Sheppard looked away for a moment, crossing his arms.

"Well, that's enough of an answer for me. Look, as soon as you take him home this can be resolved. So gear up and let's finish this."

"Yes sir."

Standing in front of the gate, Sheppard's earlier bad feeling returned as he saw Dimitri Logan approach him. They merely nodded to each other, when the wormhole opened up. With his team, John stepped through the gate, none of them expecting what would happen on the other side.


	10. Enemy

_Instinct_

_Chapter 10: Enemy_

"Alright, where are they?" Sheppard said as they entered the still visibly deserted village.

"I did mention secret places, Colonel." Dimitri smiled, heading towards a group of small buildings.

"So where's the secret passage, then?"

"That way," he pointed at the middle building then continued, "You know, it's a shame about Elizabeth. She's a good girl; I think I actually had something with her."

"What?" Sheppard spat out, visibly tensing as he turned to face him.

How the hell did Dimitri know about Elizabeth's condition? No one had told him about Elizabeth's condition, under his orders. What made it worse was the way he talked about her, it made Sheppard sick.

Dimitri was more than willing to explain everything John wanted to know when someone's voice came through John's ear piece.

"Excuse me," John said agitated, stepping out of the group's hearing range. "This better be good because-"

"I'm afraid it's the opposite." Carson Beckett's soft yet sad voice continued, "I ran some more tests but they all returned with the same result. There's an unknown toxin in Dr. Weir's bloodstream. It appears to have been there for a few days."

"How did it get there?"

"I can't say for sure, but I believe it was deliberate. There's a very large amount."

"Can you give her anything else?" John said, running a hand through his hair, his resolve wavering between anger and depression.

"I'm sorry, John. She hasn't responded to anything. There's nothing more I can do for her."

The minute John heard the news he clenched his fists tightly, as he thought it would stop him from doing the unthinkable. But it didn't, and for the first time in this ordeal, John Sheppard had a tear running down his face.

His voice was shaky when he finally spoke again, "Are you she…?"

"Just hurry, Lad. I can't guarantee anything. I'm very sorry." Carson's sympathetic tone left John alone in his sorrow.

He wanted to dial the gate and run to her side this very minute, but he knew he couldn't when he remembered the group standing a few feet behind him. She needed him, but at this moment he needed her more. John needed her to wake up and be waiting for him when he returned. He'd walk up to her calmly, them wrap his arms around her and not let go, regardless of how many people were watching. Maybe they'd have a party later to celebrate, they still had some wine…wine, why was that important?

The instant John thought of the wine he snapped back to reality. He blamed himself for letting this happen to her. He was supposed to protect her, damn it. Turning to face the group, he had one thing on his mind.

Dimitri was caught off guard finding himself pinned on the ground as John's fist connected with his jaw.

"You son of a bitch, you bastard!" Sheppard screamed, thoroughly shocking Lorne and his men as they tried to pull him off Dimitri.

"Sheppard, what the hell are you doing!" Lorne yelled, with little luck in trying to restrain him.

John launched himself at Dimitri savagely, getting more than a few punches in before some men finally pinned him to the ground. Dimitri lay on the ground with a blank expression, pushing away the men trying to help him up.

"He…he did it!"

"Did what?" Lorne asked, lost.

"Tell them, Dimitri." John nodded his head and gritting his teeth while Lorne let him sit up, "Tell them how you poisoned her."

"Well, Mister Sheppard, since you seem to have all the answers, why don't you." He retorted calmly.

"You put it in her drink; I was sitting right next to her."

Dimitri slowly lifted himself off the ground, wiping blood away from the corner of his mouth. He began to laugh when he spoke, "Took you a while to figure it out."

Lorne released Sheppard as every man circled him, raising their guns. Dimitri didn't seem stunned at all; in fact he was quite the opposite.

John stood directly in front him, handgun aimed at his temple, "Give me one reason why I shouldn't kill you right now."

"Well, I suppose they wouldn't like it very much."

Less than a second after Dimitri spoke, Sheppard and the team found themselves surrounded and out numbered as they exchanged unknowing looks. The real surprise came when they realized who they were…members of the Genii.


	11. Sacrifice

_Instinct_

_Chapter 11: Sacrifice_

"Guess you never saw this coming." Dimitri taunted Sheppard with a sickening smile. The Atlantis team had been taken underground and put in separate prison-like cells. Stripped of their weapons and gear, not only were they unable to contact Atlantis, they were vulnerable and completely at the control of the Genii. Dimitri took the liberty of locking Sheppard up, presumably so he could gloat over that fact that his scheme was successful.

"Guess not." John grimaced, "You knew what would happen to her."

"Elizabeth was an unfortunate casualty."

"Her name is Dr. Weir." John corrected sternly.

"That's not what you call her." Sheppard tensed at the tone of Dimitri's voice. He was playing on his emotions; John knew he couldn't let it get to him, but it was hard to keep straight face.

"I seem to have hit a nerve." Dimitri observed casually, "I know this isn't important, but I'm curious, how is she?"

"She's dying."

"I think you know what I mean."

"How would I know?" John asked calmly, though inside he felt like a raging river. He couldn't believe what Dimitri was doing.

"Oh, come on, Sheppard. You expect me to believe that you two haven't…"

"No, we haven't." John cut him off with an angry glare.

"That's too bad. Maybe I should've added a little more time for fun."

"She never would've done that."

"Maybe you don't know her as well as you think."

"What's the point of all this?" Sheppard broke, unable to handle Dimitri's insinuating speech. He needed to change the subject and as much as it hurt, get Elizabeth off his mind.

"This, this is nothing. The bigger plan that you played into, quite easily I might add; that is unfolding as we speak."

"I never trusted you."

"I didn't need you to trust me. I just needed you to listen."

The day went by slower than ever. John sat in his cell thinking of escape plans, none of them seeming like they would work. It was his fault…everything. Shaking his head, he sighed. He had to make it right and he would, if he ever got out of here. A door opening caught his attention. The man stopping in front of his cell surprised him.

"Hey, Sheppard," He said; hardly any energy in him.

"Lorne, what's going on?"

"They're letting me go. To negotiate a trade."

"A trade for what?" John asked excited, walking towards the bars.

"John, they have an antidote. They can save Dr. Weir."

John's mouth dropped. An antidote. Saved. Was this possible or was it another trick? It had to be real, they were letting Lorne go. He was overjoyed that one of men was being freed, but it brought on more questions. Why would they just let him go? What would the trade be for? What could they possibly want that they didn't already have? Though, in an instant it hit him. They did have what they want.

"Lorne, the trade, it's for me, isn't it?"

"According to Logan, if they get to keep you, then they'll send the antidote. I'm sorry; I tired to make them choose me instead…"

"I know. You did everything you could. But this is way it has to be. Now I'm ordering you, go to Atlantis and make Caldwell take the deal."

"Are you serious, you're giving in, just like that? You know what they'll do to you?"

"It doesn't matter. What does is the fact that Elizabeth will live."

"Yeah, without you. How do you think she's going to take that?"

"She's strong, she'll move on. She knows I'd do anything for her, even this."

"I can't do this." Lorne muttered.

"Yes, you can and you will. I made it an order. And you damn well better follow them, especially if they're going to be my last."

"Yes, sir." Lorne answered with a strict face before walking away. Shooting one last sympathetic look at Sheppard.

John heard the door close and sat back down. He knew what he was doing, it was the right thing. Elizabeth would live because of it. That was worth everything. When he joined this expedition he never thought he'd make the ultimate sacrifice, especially for a woman….a woman he loved. He didn't regret what he just said to Lorne. He intended to follow through. There was only one thing he did regret; that he couldn't hold Elizabeth at this very moment and tell her exactly what he felt.

a/n: Sorry for the wait guys! Been really busy. Thanks for all the reviews, I love them! Hope you enjoyed this, I know it's short. I've got to get ready for school again, so a lot of other things are on my mind right now. That sucks.


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